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ENIAC could be programmed to perform complex sequences of operations, including loops, branches, and subroutines. However, instead of the stored-program computers that exist today, ENIAC was just a large collection of arithmetic machines, which originally had programs set up into the machine by a combination of plugboard wiring and three portable function tables (containing 1200 ten-way switches each). The task of taking a problem and mapping it onto the machine was complex, and usually took weeks. Due to the complexity of mapping programs onto the machine, programs were only changed after huge numbers of tests of the current program. After the program was figured out on paper, the process of getting the program into ENIAC by manipulating its switches and cables could take days. This was followed by a period of verification and debugging, aided by the ability to execute the program step by step. A programming tutorial for the modulo function using an ENIAC simulator gives an impression of what a program on the ENIAC looked like.

Kay McNulty, Betty Jennings, Betty Snyder, Marlyn Meltzer, Fran Bilas, and Ruth Lichterman were the first programmers of the ENIAC. They were not, as computer scientist and historian Kathryn Kleiman was once told, "refrigerator ladies", i.e., models posing in front of the machine for press photography. Nevertheless, some of the women did not receive recognition for their work on the ENIAC in their lifetimes.

These early programmers were drawn from a group of about two hundred women employed as computers at the Moore School of Electrical Engineering at the University of Pennsylvania. The job of computers was to produce the numeric result of mathematical formulas needed for a scientific study, or an engineering project. They usually did so with a mechanical calculator. This was one of the few technical job categories available to women at that time. Betty Holberton (nee Snyder) continued on to help write the first generative programming system (SORT/MERGE) and help design the first commercial electronic computers, the UNIVAC and the BINAC, alongside Jean Jennings. McNulty developed the use of subroutines in order to help increase ENIAC's computational capability.

Herman Goldstine selected the programmers, whom he called operators, from the computers who had been calculating ballistics tables with mechanical desk calculators, and a differential analyzer prior to and during the development of ENIAC. Under Herman and Adele Goldstine's direction, the computers studied ENIAC's blueprints and physical structure to determine how to manipulate its switches and cables, as programming languages did not yet exist. Though contemporaries considered programming a clerical task and did not publicly recognize the programmers' impact on the successful operation and announcement of ENIAC, McNulty, Jennings, Snyder, Wescoff, Bilas, and Lichterman have since been recognized for their contributions to computing.

The "programmer" and "operator" job titles were not originally considered professions suitable for women. The labor shortage created by World War II helped enable the entry of women into the field. However, the field was not viewed as prestigious, and bringing in women was viewed as a way to free men up for more skilled labor. For example, the National Advisory Committee for Aeronautics said in 1942, "It is felt that enough greater return is obtained by freeing the engineers from calculating detail to overcome any increased expenses in the computers' salaries. The engineers admit themselves that the girl computers do the work more rapidly and accurately than they would. This is due in large measure to the feeling among the engineers that their college and industrial experience is being wasted and thwarted by mere repetitive calculation".

Although the Ballistic Research Laboratory was the sponsor of ENIAC, one year into this three-year project John von Neumann, a mathematician working on the hydrogen bomb at Los Alamos National Laboratory, became aware of this computer. Los Alamos subsequently became so involved with ENIAC that the first test problem run consisted of computations for the hydrogen bomb, not artillery tables. The input/output for this test was one million cards.

Related to ENIAC's role in the hydrogen bomb was its role in the Monte Carlo method becoming popular. Scientists involved in the original nuclear bomb development used massive groups of people doing huge numbers of calculations ("computers" in the terminology of the time) to investigate the distance that neutrons would likely travel through various materials. John von Neumann and Stanislaw Ulam realized the speed of ENIAC would allow these calculations to be done much more quickly. The success of this project showed the value of Monte Carlo methods in science.